The two terms are different, simply because the word pandit, which is Pundit in English also exists as a separate term in Bahasa Melayu, 'Pendita'.
A Pendita is someone of high esoteric knowledge, usually non-combat related, a thinker, a scholar and is a much older term used to describe sages and saints before the coming of Islam.
Today, Pendita is used to socially anoint great Melayu thinkers. A famous example is Pendita Zaaba, our late father of the modern Melayu language, who was active in the mid-20th century.
Recently also, the Malaysian martial arts community, through the SENI BELADIRI martial arts magazine, have unofficially titled guru Anwar Wahab with Pendita, the founder of the modern form of Seni Gayung Fatani, who is known as a scholar of silat in general.